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Messages
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Messages - Matthew Keller
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MS-DIAL / InChIKey Generation
There seems to be a bug in the InChiKey generation. I'm getting a few InChiKeys that don't seem to match their corresponding metabolite. At least, they pull up 0 results on Pubchem. It looks like they should have a S instead of an N in the third position from the end. I listed a few examples below.
Name MS-DIAL Generated InChIKey Correct(?) InChIKey
3-Hydroxyvaleric acid REKYPYSUBKSCAT-UHFFFAOYNA-N REKYPYSUBKSCAT-UHFFFAOYSA-N
Leucine ROHFNLRQFUQHCH-UHFFFAOYNA-N ROHFNLRQFUQHCH-UHFFFAOYSA-N
Pyroglutamic acid ODHCTXKNWHHXJC-UHFFFAOYNA-N ODHCTXKNWHHXJC-UHFFFAOYSA-N
Threonine AYFVYJQAPQTCCC-UHFFFAOYNA-N AYFVYJQAPQTCCC-UHFFFAOYSA-N
Could this be easily patched, or is there a workaround? I guess I could use the SMILES instead of the InChIKeys.
Thanks!
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Vendor specific software / Compound Discoverer Bug
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MS-DIAL / Re: Few MS Annotations
Thanks for the advice, opening up the MS2 accuracy helped a lot. A separate issue I had is that MS-DIAL seemed to be picking some shoulders and dropping the rest of the peak. Do you have any suggestions for that? For some of these, it looked like MS-DIAL was expecting the peak widths to be shorter than they were, is there a way to change that?
Also, I would have uploaded an .abf in case that would be helpful, but I wasn't sure how to do that.
Thanks,
Matthew
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MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
I think I can answer C and D for you. C, If you want to annotate a feature by hand, you can click the spot and then "show ion table," from here you can type whatever you like into the comment box. If I understand you're asking, that should help. D, if you're doing SWATH or something similar, the deconvolution works by matching EICs of fragment ions with that of parent features. Fragments that have similar EICs are displayed as the deconvoluted MS2 of that feature. The MS-DIAL paper has more details.
~Matthew
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MS-DIAL / Re: Few MS Annotations
Thanks for the advice. We do have the LTQ scanning the MS2 and the Orbi for MS1. However, in our setup, both the LTQ and Orbitrap are in centroid mode. I've tried various values for the MS2 accuracy and identification parameters, but haven't improved things. Is there a guide or something regarding how to optimize parameters for MS2 level annotation?
Thanks,
Matthew
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MS-DIAL / Few MS Annotations
I'm trying to process a DDA lipidomics sample set I have and after running identification, I'm getting a lot a MS1 annotations (without MS2), but very few assignments that use the MS2s (164 vs . Looking at the data by hand, the MS2 look to be of at least moderate quality, so I'm not sure why there would be so few MS2 annotations.
Has this happened to anyone else? Do you know what parameters might need to be adjusted? I'm using an LTQ-Orbitrap in case that's relevant.
Thanks,
~Matthew
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MS-DIAL / Re: Library Installation Error
Thanks for the clarification, I got it working now.
Matthew
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MS-DIAL / Library Installation Error
I am trying to get MS-DIAL started to compare it to other metabolomics programs and I downloaded library files from the MS-DIAL homepage http://prime.psc.riken.jp/compms/msdial/main.html#MSP. After trying to run the .msp file, I got the error: THIS PATCH PACKAGE COULD NOT BE OPENED. Has this happened to anyone else? Any advice?
Thanks!
Matthew